OOIR: Observatory of International Research

Papers

(The H4-Index of Microbiome is 70. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)

Article	Citations
Microbiome definition re-visited: old concepts and new challenges	853
Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank	478
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences	474
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses	434
Review: microbial transformations of human bile acids	285
Gut microbiota from green tea polyphenol-dosed mice improves intestinal epithelial homeostasis and ameliorates experimental colitis	261
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes	239
Specialized metabolic functions of keystone taxa sustain soil microbiome stability	212
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity	205
Low shifts in salinity determined assembly processes and network stability of microeukaryotic plankton communities in a subtropical urban reservoir	191
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens	182
Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression	176
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition	173
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks	167
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance	166
Plant developmental stage drives the differentiation in ecological role of the maize microbiome	164
Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories	161
Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-br	161
Disease-induced changes in plant microbiome assembly and functional adaptation	157
Disentangling the mechanisms shaping the surface ocean microbiota	153
Using soil bacterial communities to predict physico-chemical variables and soil quality	139
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2	139
Lung function and microbiota diversity in cystic fibrosis	136
Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients	131
β-glucan attenuates cognitive impairment via the gut-brain axis in diet-induced obese mice	125

Syntrophic acetate oxidation replaces acetoclastic methanogenesis during thermophilic digestion of biowaste	120
Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes	120
Rhizosphere community selection reveals bacteria associated with reduced root disease	112
Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia	111
Gut microbiome composition differences among breeds impact feed efficiency in swine	110
Gut microbiota-derived indole 3-propionic acid protects against radiation toxicity via retaining acyl-CoA-binding protein	110
Direct impact of commonly used dietary emulsifiers on human gut microbiota	110
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants	108
From gut microbiota to host appetite: gut microbiota-derived metabolites as key regulators	107
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics	106
Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain	105
Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation	102
Thousands of previously unknown phages discovered in whole-community human gut metagenomes	101
Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula	100
Challenges in exploring and manipulating the human skin microbiome	99
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas	99
Prevotella copri increases fat accumulation in pigs fed with formula diets	99
Endometrial microbiota composition is associated with reproductive outcome in infertile patients	98
Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration	98
Host habitat is the major determinant of the gut microbiome of fish	98
TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila	97
Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease	96
Effect of fecal microbiota transplantation on neurological restoration in a spinal cord injury mouse model: involvement of brain-gut axis	95
The extracellular vesicle of gut microbial Paenalcaligenes hominis is a risk factor for vagus nerve-mediated cognitive impairment	93
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin	93
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data	87
A fiber-deprived diet causes cognitive impairment and hippocampal microglia-mediated synaptic loss through the gut microbiota and metabolites	87
Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils	86
Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice	86
Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers	84
A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community	83
Gut microbiota modulation with long-chain corn bran arabinoxylan in adults with overweight and obesity is linked to an individualized temporal increase in fecal propionate	81
A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota	81
The microbiome and mosquito vectorial capacity: rich potential for discovery and translation	81
Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios	81
Identifying biases and their potential solutions in human microbiome studies	80
A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance	78
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases	77
Towards enhancing coral heat tolerance: a “microbiome transplantation” treatment using inoculations of homogenized coral tissues	76
Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease	76
The microbial metabolite p-Cresol induces autistic-like behaviors in mice by remodeling the gut microbiota	75
Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer	75
Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice	74
Protists as main indicators and determinants of plant performance	72
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria	72
Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models	70
Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status	70